MolNFT v1 · #119361 · protein
Octameric complex of latrophilin 3 (lec, olf) , UNC5D (ig, IG2, TSP1) and FLRT2 (lrr)
5FTT · Netrin receptor UNC5D: “Octameric complex of latrophilin 3 (lec, olf) , UNC5D (ig, IG2, TSP1) and FLRT2 (lrr)”. X-ray diffraction, 3 ligands (NAG, NA, CA), 20 pockets (best druggability 0.83). MolNFT v1 #119361 on GenesisL1: 3D…
- PDB
- 5FTT
- Type
- protein
- Length
- 2,436 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin receptor UNC5D; Leucine-rich repeat transmembrane protein FLRT2; Adhesion G…
- UniProt
- F1LW30, Q8BLU0, Q80TS3
- Ligands
- NAG, NA, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin receptor UNC5D | protein | 262 | 3% helix, 39% strand | F1LW30 |
| B | Leucine-rich repeat transmembrane protein FLRT2 | protein | 326 | 10% helix, 17% strand | Q8BLU0 |
| C | Adhesion G protein-coupled receptor L3 | protein | 365 | 5% helix, 45% strand | Q80TS3 |
| D | Adhesion G protein-coupled receptor L3 | protein | 263 | 3% helix, 47% strand | Q80TS3 |
| E | Netrin receptor UNC5D | protein | 259 | 3% helix, 43% strand | F1LW30 |
| F | Leucine-rich repeat transmembrane protein FLRT2 | protein | 332 | 10% helix, 17% strand | Q8BLU0 |
| G | Adhesion G protein-coupled receptor L3 | protein | 368 | 5% helix, 46% strand | Q80TS3 |
| H | Adhesion G protein-coupled receptor L3 | protein | 261 | 2% helix, 49% strand | Q80TS3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, E, F, G
- NA · Sodium ion · metal · 4 copies · chains C, D, G, H
- CA · Calcium ion · metal · 4 copies · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.83 | 0.85 | 109 | empty |
| 2 | 876 | 0.82 | 0.84 | 95 | empty |
| 3 | 877 | 0.82 | 0.84 | 97 | empty |
| 4 | 820 | 0.81 | 0.84 | 100 | empty |
| 5 | 314 | 0.64 | 0.80 | 56 | empty |
Interfaces
14 interfaces between chains.
- A–E · 1545 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 922 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 871 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 789 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 753 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5FTT · Octameric complex of Latrophilin 3 (Lec, Olf) , Unc5D (Ig, Ig2, TSP1) and FLRT2 (LRR) · the same entry in another collection · chain H against H, TM-score 1.00
- Q80TS3 · AlphaFold monomer V2.0 prediction for adhesion G protein-coupled receptor L3 (Q80TS3) · a predicted model of the same protein · chain H against A, TM-score 0.99
- Q8BLU0 · AlphaFold monomer V2.0 prediction for leucine-rich repeat transmembrane protein FLRT2… · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F1LW30
- Every structure of UniProt Q8BLU0
- Every structure of UniProt Q80TS3
- Elsewhere: RCSB PDB 5FTT · PDBe 5FTT · UniProt F1LW30 · UniProt Q8BLU0 · UniProt Q80TS3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.